High-Speed Atomic Force Microscopy Reveals Spontaneous Nucleosome Sliding of H2A.Z at the Subsecond Time Scale

Unraveling dynamics of nuclear pore and chromatin via HS-AFM

High-speed atomic force microscopy (HS-AFM) enables real-time visualization of biological processes with nanometer-level resolution. This review highlights how HS-AFM has been instrumental in uncovering the dynamic interplay between nuclear pore complexes (NPCs)-which regulate nucleocytoplasmic transport-and genome guardians, including DNA repair proteins and chromatin regulators. Structurally, the NPCs resemble a multi-layered spider cobweb, serving as crucial molecular gatekeepers for maintaining cellular homeostasis, while genome guardians safeguard genomic integrity through DNA repair and chromatin organization. Through HS-AFM, the researchers have gained unprecedented insights into NPC dynamics, revealing their adaptability during nuclear transport, chromatin reorganization, and viral infection. It has also elucidated how genome guardians interact with NPCs, influencing chromatin organization at the nuclear periphery and regulating nucleocytoplasmic trafficking. These discoveries underscore the critical role of NPC-genome interactions in genome stability, gene expression, and nuclear transport, with broad implications for diseases such as cancer, viral infections, and neurodegenerative disorders. In conclusion, HS-AFM has transformed our ability to study the nuclear landscape at the nanoscale, bridging the gap between structural biology and functional genomics. By capturing the real-time molecular dynamics of NPCs and chromatin, HS-AFM provides an essential tool for unraveling the mechanisms that govern nuclear transport and genome regulation. Future advancements in HS-AFM technology, including higher temporal resolution, correlative imaging, and AI-driven analysis, will further expand its potential in biomedical research, paving the way for novel diagnostic and therapeutic strategies.

The "Ins and Outs and What-Abouts" of H2A.Z: A tribute to C. David Allis

In 2023, the brilliant chromatin biologist C. David Allis passed away leaving a large void in the scientific community and broken hearts in his family and friends. With this review, we want to tribute Dave's enduring inspiration by focusing on the histone variant H2A.Z, a nucleosome component he was the first to discover as hv1 in Tetrahymena. We summarize the latest findings from the past 5 years regarding the mammalian H2A.Z histone, focusing on its deposition and eviction mechanisms, its roles in transcriptional regulation, DNA damage repair, chromatin structure organization, and embryonic development, as well as how its deregulation or mutation(s) of its histone chaperones contribute to disease development. As Dave liked to say 'Every amino acid matters'; the discovery and characterization of functionally different H2A.Z's isoforms, which vary only in three amino acids, prove him-once again-right.

Epigenetic modulation via the C-terminal tail of H2A.Z

H2A.Z-nucleosomes are present in both euchromatin and heterochromatin and it has proven difficult to interpret their disparate roles in the context of their stability features. Using an in situ assay of nucleosome stability and DT40 cells expressing engineered forms of the histone variant we show that native H2A.Z, but not C-terminally truncated H2A.Z (H2A.Z∆C), is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations. H2A.Z and H3K9me3 landscapes are reorganized in H2A.Z∆C-nuclei and overall sensitivity of chromatin to nucleases is increased. These tail-dependent differences are recapitulated upon treatment of HeLa nuclei with the H2A.Z-tail-peptide (C9), with MNase sensitivity being increased genome-wide. Fluorescence correlation spectroscopy revealed C9 binding to reconstituted nucleosomes. When introduced into live cells, C9 elicited chromatin reorganization, overall nucleosome destabilization and changes in gene expression. Thus, H2A.Z-nucleosomes influence global chromatin architecture in a tail-dependent manner, what can be modulated by introducing the tail-peptide into live cells.

Single-Macromolecule Studies of Eukaryotic Genomic Maintenance

Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.

High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes

Each nucleosome contains four types of histone proteins, each with a histone tail. These tails are essential for the epigenetic regulation of gene expression through post-translational modifications (PTMs). However, their influence on nucleosome dynamics at the single-molecule level remains undetermined. Here, we employed high-speed atomic force microscopy to visualize nucleosome dynamics in the absence of the N-terminal tail of each histone or all of the N-terminal tails. Loss of all tails stripped 6.7 base pairs of the nucleosome from the histone core, and the DNA entry-exit angle expanded by 18° from that of wild-type nucleosomes. Tail-less nucleosomes, particularly those without H2B and H3 tails, showed a 10-fold increase in dynamics, such as nucleosome sliding and DNA unwrapping/wrapping, within 0.3 s, emphasizing their role in histone-DNA interactions. Our findings illustrate that N-terminal histone tails stabilize the nucleosome structure, suggesting that histone tail PTMs modulate nucleosome dynamics.

Role of Nucleosome Sliding in the Protein Target Search for Covered DNA Sites

Associations of transcription factors (TFs) with specific sites on DNA initiate major cellular processes. But DNA in eukaryotic cells is covered by nucleosomes which prevent TFs from binding. However, nucleosome structures on DNA are not static and exhibit breathing and sliding. We develop a theoretical framework to investigate the effect of nucleosome sliding on a protein target search. By analysis of a discrete-state stochastic model of nucleosome sliding, search dynamics are explicitly evaluated. It is found that for long sliding lengths the target search dynamics are faster for normal TFs that cannot enter the nucleosomal DNA. But for more realistic short sliding lengths, the so-called pioneer TFs, which can invade nucleosomal DNA, locate specific sites faster. It is also suggested that nucleosome breathing, which is a faster process, has a stronger effect on protein search dynamics than that of nucleosome sliding. Theoretical arguments to explain these observations are presented.